Lambda Moses
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/BUSpaRse |
| Branch: master |
| Last Commit: ec7070a |
| Last Changed Date: 2019-10-29 13:43:38 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:55:08 -0500 (Thu, 16 Jan 2020).
| Package 210/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BUSpaRse 1.1.0 Lambda Moses
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: BUSpaRse |
| Version: 1.1.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BUSpaRse_1.1.0.tar.gz |
| StartedAt: 2020-01-16 02:23:26 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 02:43:54 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 1228.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BUSpaRse.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BUSpaRse_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BUSpaRse.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BUSpaRse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BUSpaRse’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BUSpaRse’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
transcript2gene 22.199 8.796 33.265
tr2g_EnsDb 14.672 4.141 19.384
tr2g_TxDb 12.176 2.608 16.385
tr2g_ensembl 3.649 0.273 507.406
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/BUSpaRse.Rcheck/00check.log’
for details.
BUSpaRse.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BUSpaRse ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘BUSpaRse’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c fill_cell_gene.cpp -o fill_cell_gene.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BUSpaRse.so RcppExports.o fill_cell_gene.o -fopenmp -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-BUSpaRse/00new/BUSpaRse/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BUSpaRse)
BUSpaRse.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(BUSpaRse)
>
> test_check("BUSpaRse")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 109 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
69.054 3.104 239.970
BUSpaRse.Rcheck/BUSpaRse-Ex.timings
| name | user | system | elapsed | |
| EC2gene | 0.250 | 0.016 | 0.270 | |
| get_velocity_files | 3.378 | 0.175 | 3.557 | |
| make_sparse_matrix | 0.008 | 0.002 | 0.012 | |
| read_count_output | 0.028 | 0.005 | 0.036 | |
| read_velocity_output | 0.021 | 0.006 | 0.027 | |
| save_tr2g_bustools | 0.177 | 0.026 | 0.205 | |
| sort_tr2g | 0.140 | 0.026 | 0.163 | |
| species2dataset | 0.002 | 0.002 | 0.001 | |
| tr2g_EnsDb | 14.672 | 4.141 | 19.384 | |
| tr2g_TxDb | 12.176 | 2.608 | 16.385 | |
| tr2g_ensembl | 3.649 | 0.273 | 507.406 | |
| tr2g_fasta | 0.014 | 0.002 | 0.017 | |
| tr2g_gff3 | 0.319 | 0.006 | 0.332 | |
| tr2g_gtf | 0.151 | 0.003 | 0.155 | |
| transcript2gene | 22.199 | 8.796 | 33.265 | |